Biography:

Abstract:

Microbial diversity in soil may be limited under natural conditions by inappropriate environmental factors such as: limited food resources, environmental and physical factors, tillage system and interspecies interactions prevent the occurrence or maintenance of the species in the environment. The aim of this work was to determinate structural biodiversity and functional microorganisms in in soil under long-term maize monoculture. The reaction of maize cultivated in perennial monoculture for the direct sowing was investigated and compared to full tillage monoculture and crop rotation full tillage cultivation in the following phases: six leaves, twelve leaves, flowering phase, before harvest and after harvest. Three objects were included into this research: maize cropped continuously monoculture - zero tillage, maize monoculture cropped continuously – full tillage, crop rotation (spring barley, winter wheat, maize) – full tillage. The evaluation of the structural biodiversity of the soil was based on the next-generation sequencing (NGS). The functional and metabolic profiles in soil were determined by Biolog EcoPlate System. The research methods used in this subject have contributed to a better understanding of genetic diversity and composition of the population of microorganisms in the soil environment under the influence of the changes that have taken in soil under long-term maize monoculture.

Biography:

Anna GaÅ‚Ä…zka is a head of the Department of Agricultural Microbiology at IUNG (since 2013). She is specialized in the evaluation of microbial diversity of soils associated with agricultural practice and environmental protection (research in molecular biology; evaluation of genetic differentiation and identification of microorganisms and characterization of metabolic profile of bacteria and fungi). She is participating in international and several national projects in IUNG, coordinating research project on biological activity and determination of microbial diversity of soil. She was a task manager in Aiming Project „Developing New system of tillage for sustainable agriculture” WND-POIG. 01.03.01-00-042/09 (2010-2013) – Determination of biological activity in soils and executor in projects: N305 080 32/2776 Evaluation of usefulness of Azospirillum spp. and Pseudomonas stutzeri inoculum in increasing of phytoremediation; project CZ.3.22/1.2.00/12.03445, Risk and benefits of application of exogenous organic matter on soil.  Operational programme of cross-border co-operation Czech Republic – Poland 2007-2013. She was training of „Genomic of Nitrogen-Fixation Organisms” in 2008, Ghent, Belgium and participated in numerous courses and trainings in the field of molecular biology and microbiology. She works with NJF Nordic Association of Agricultural Scientists (keynote speakers on Seminar (483) 22-25.09.2015 Vezaiciai, Lithuania “Application of soil biological and biochemical parameters as indicator of soil health and fertility as influenced by different agrotechnical practices”). Member of Polish Microbiological Society since 2004 and author over 50 publications.

Abstract:

Soil contamination with crude oil, especially in the area of oil wells, is a serious environmental problem. Restoring the long – term pollution soil to its original state is very difficult. Under such conditions, the unique group of bacterial communities develops in the soil. This communities  are  adapted to the contamination conditions. Analysis of the structure and function of these microorganisms can be a source of valuable information. The aim of the study was to evaluate functional and structural diversity of bacterial communities in soils with long term impacts from crude oil. Samples were taken from four oil wells: one oldest and still working (W01, working from 1888) and three younger (W02, W03, W04, working from the beginning of 20th century) still working but with periodic breaks – these oil wells works only few months every years. Soil samples were collected at two distances: within a radius of 0.5 m of the oil wells (W01R, W02R, W03R, W04R) and within a radius of 3 m from the oil wells (W01, W02, W03, W04). The next generation sequencing technique (V3-V4 16S rRNA) was accompanied with the community level physiological profiling (CLPP) method in order to better understand knowledge of both genetic and functional structure of soils collected under several oil wells. The significant differences of bacterial community structure between soils were obtained. The soils taken directly from oil wells were characterized by different composition of bacteria. The highest activity of carbon utilization patterns were observed in soils taken directly from oil wells.

Biography:

Antoni Lichev has finished his Bachelor’s and his Master’s Thesis in Molecular Biotechnology at the Technical University of Munich. Since 2015 he has been doing his PhD in Microbiology at the Department of Microbiology at the Technical University of Munich. His previous work has been published in the journal “Frontiers in Microbiology”.

Abstract:

Natural genetic transformation has been documented in more than 80 bacterial species, including members of nearly all major taxonomic groups. Being one of the main routes for horizontal gene transfer, this process incorporates the internalization and the chromosomal integration of exogenous DNA during a genetically preprogrammed differentiated state called competence. In spite of the longstanding investigation of this phenomenon, so far only little is known about the regulatory mechanisms involved in genetic transformation and notably so in the case of representatives of the Actinobacteria phylum (high GC Gram-positive bacteria). In this report we focus on the competence development in the Actinobacteria member Micrococcus luteus. We provide evidence that nutritional limitation, provoked by the absence of amino acids in the growth medium, induces natural transformation in this species. Paradoxically, we also show that amino acid auxotrophy strongly inhibits competence development. We demonstrate the negative impact of a deletion of a RelA/SpoT-like homologue (Mlut_12840) and a putative novel (p)ppGpp synthetase (Mlut_22200) on natural transformation and we therefore speculate the involvement of the stringent response in the complex regulation of the competent state of Micrococcus luteus. Furthermore we investigate the specific regulatory function of branched-chain amino acids (BCAAs) and signify them as modulators of competence that alter expression of transformation-related genes. To our knowledge our data provides the first general insights into the regulation of natural transformation in a member of the Actinobacteria phylum and may also prove to be pertinent to a number of important pathogens belonging to the same taxonomic group.

Biography:

Jungkwan Lee has completed his Ph.D. from Kansas State University, USA and postdoctoral studies from Seoul National University, Korea. He is an associate professor in Dong-A University, Korea. He has been working in the interaction between plant pathogenic fungi and bacteria in rice plants. He published more than 40 papers in reputed journals and has been serving as an associate editor for The Plant Pathology Journal.

Abstract:

The air-borne ascomycete fungus Fusarium graminearum causes head blight in many cereals and produces mycotoxins such as trichothecenes and zearalenone. The seed-borne bacterium Burkholderia glumae causes bacterial panicle blight in rice and produces toxolavin that has antimicrobial activity and phytotoxicity. Disease symptoms caused by two pathogens are very similar and could often cause false diagnosis. In this study, we showed that two pathogens frequently co-isolated in rice heads and F. graminearum is resistant to toxoflavin produced by B. glumae while other fungal genera are sensitive to the toxin. We have tried to clarify the resistant mechanism of F. graminearum against toxoflavin and the ecological reason of co-existence of the two pathogens in rice. We found that F. graminearum resistance to toxoflavin is related to production of triacylglycerides containing linolenic acid. Co-cultivation of two pathogens resulted in increased conidia and trichothecene by F. graminearum. Bacteria physically attached to fungal conidia, which protected bacterium cells from UV light and allowed disease dispersal. Chemotaxis analysis showed that bacterial cells moved toward the fungal exudation. Disease severity on rice heads was significantly increased by co-inoculation rather than single inoculation. This study provides evidence of the two pathogens cooperatively interacting, with F. gramienarum gaining the opportunity to induce disease progression efficiently and B. glumae achieving aerial dispersal.

Biography:

Kamontam Umsakul associated with Department of Microbiology, Prince of Songkla University , Thailand. She has published several papers in reputed journals.  Her research interest is Microbiology.

Abstract:

An increasing production of natural rubber (NR) products has led to major challenges in waste management since the degradation of NR is normally extremely slow. In this study, the degradation of rubber latex gloves in a mineral salt medium (MSM) using a natural soil consortium was studied. Soil consortia can degrade rubber gloves much more quickly than those of the single culture using the same conditions. The weight loss of the rubber gloves after incubation with a soil consortium of up to 14 days was as high as 59%. In contrast with using a single strain, only 9% of rubber glove weight loss was obtained. Determination of carbon dioxide evolution and viable cell number during cultivation with rubber gloves as a sole carbon source, revealed mineralization of the rubber materials during the increase of biomass. Scanning electron microscopy demonstrated an adhesive growth behavior of the consortium on the rubber surfaces. The results from Fourier transform infrared spectroscopy revealed the decrease in number of cis-1,4 double bonds, the formation of carbonyl groups indicating an oxidative attack at the double bonds.

Biography:

MaÅ‚gorzata Woźniak obtained a master degree in biology with specialization microbiology in 2015. She studied at Maria Curie-SkÅ‚odowska University (UMCS) in Lublin, Poland.  She work in Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation in Poland. She is principal Investigator (head of the project) in two projects: the research project in the statutory activity of IUNG-PIB, Title of project: "Molecular and biochemical identification of the endophytic bacteria and it application in plant growth promoting” and Preludium project, the National Science Center, Title of project: “The influence of fast-growing Paulownia Clon In Vitro 112 (P.elonagata x P.fortunei) on microbiological and physico-chemical properties of the soil in Poland”).

Abstract:

The Paulownia spp. is a fast growing variety of deciduous tree that belongs to the Paulowniaceae family. These trees are used to produce biomass and reduce carbon dioxide concentrations in the atmosphere. Paulownia spp. leaves have a high content of protein, fats, sugar and nitrogen, phosphorus, potassium (NPP). The purpose of this study was to determine the functional and genetic diversity of the microbial of the Paulownia spp. Next Generation Sequencing (NGS) and Biolog EcoPlates were used to evaluate microbial diversity. The research materials were leaves of trees Paulownia spp. Plant samples were taken from Podkampinos (a plantation established on arable soil) and OtrÄ™busy (a plantation established on degraded soil). The samples were the clones of the same hybrid Paulownia elongata and Paulownia fortunei. Additional hybrid of Paulownia tomentosa and Paulownia fortunei was included. The functional analysis was carried out using statistical methods: cluster analysis by Ward’s method, taking into account Euclidean square of distance. Moreover, the Shannon-Wiener (H') biodiversity index, R Richness, E Evenness, and AWCD (average well color development) were calculated. The obtained sequences were subject to bioinformatics analyses, such as clustering and separation of operational taxonomic units (OTU). The samples from the plantation established on degraded soli revealed that the most dominant phylum was Bacteroidetes, whereas from the arable soil, Proteobacteria. Comparisons of carbon source utilization and the diversity indices showed differences in the microbial community of composition. Among the five carbon sources studied, carbohydrates were the most frequently used group of compounds.

This research funded by the NCN-Preludium project no 2016/23/N/NZ9/02157

Biography:

MaÅ‚gorzata Woźniak obtained a master degree in biology with specialization microbiology in 2015. She studied at Maria Curie-SkÅ‚odowska University (UMCS) in Lublin, Poland.  She work in Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation in Poland. She is principal Investigator (head of the project) in two projects: the research project in the statutory activity of IUNG-PIB, Title of project: "Molecular and biochemical identification of the endophytic bacteria and it application in plant growth promoting” and Preludium project, the National Science Center, Title of project: “The influence of fast-growing Paulownia Clon In Vitro 112 (P.elonagata x P.fortunei) on microbiological and physico-chemical properties of the soil in Poland”).

Abstract:

Bacterial endophytes reside in a large number of plant species as part of their microbiome. Endophyte community structure exhibits a high diversity of species within a plant. This diversity is determined by abiotic and biotic factors such as soil conditions, biogeography, plant species, microbe– microbe interactions and plant–microbe interactions. The purpose of this study was to assess the degree of genomic diversity, relationship and molecular identification of bacteria isolated from the endosphere of maize, broad bean, wheat, rye, horsetail and burdock (root and stem). The tests were performed on 45 strains. The genetic identification of bacterial population was performed based on comparative sequence analysis of the 16S rDNA. On the basis of 16S ribosomal RNA sequences, all strains of  bacteria were assigned to 10 genera: Rhizobium (19 isolates), Delftia (11 isolates), Agrobacterium (5 isolates), Stenotrophomonas (3 isolates), Brevundimonas (2 isolates), Novosphingobium (1 isolate), Variovorax (1 isolate), Collimonas (1 isolate), Achromobacter (1 isolate) and Comamonas (1 isolate). The assessment of the diversity of potential plant growth promoting bacteria, including 11 species Delftia sp, was conducted based on the BOX-PCR, ERIC-PCR and PCR-DGGE techniques. The genetic profile shows similarity among tested bacteria strains. The microorganism group was related to the type of the host plant.

This research was supported by the project nr 1.21 (2017 – 2019) the statutory activity of IUNG-PIB in Pulawy "Molecular and biochemical identification of endophytic bacteria and their use in plant growth promotion".

Biography:

Martina Franchini main interests in Biology have driven her to concentrate her studies in the microbiological field. During the years, her expertise has been focused on the investigation of the environmental main issues and how Biology, and more specifically, Microbiology, can approach them. Bioremediation has been the subject of her latest studies: from the use of bacteria for reduction of toxic oxianions with concurrent bioproduction of Nanoparticles to a participation in a study aimed to isolate a bacterial consortium of plastic biodegraders.

Martina has worked in international contexts, learning the importance of constructive team work and open knowledge sharing.

Abstract:

Gluconacetobacter diazotrophicus (Gd) is a non-nodulating endophytic nitrogen-fixing bacterium isolated from the intercellular spaces of sugarcane. The aim of this study was to investigate the effect of this bacterium on Tomato plants in presence and absence of Trichoderma asperellum (T34 commercial strain). Trichoderma spp. is one of the most widely employed biological control agents used against plant pathogens and is an opportunistic avirulent plant symbiont. This fungus is known to antagonize other soil fungi either parasitizing on them or inhibiting their growth due to the production and release of cell wall degrading enzymes. Furthermore, T. asperellum has been shown to synthetize a wide range of other plant protective molecules that can enhance the plant’s response to pathogens. However, the details of its modes of action still remain to be clarified.

To investigate the effect of the combined action of T34 and Gd on crop plants, Tomato Money Maker seeds were treated with Gd and sown into Levington M3 soil in presence and absence of T. asperellum. T34 biocontrol agent from FarGro® was mixed to the soil before sowing.

Four months after sowing, differences in plants’ strength and biomass production were observed: plants grown in presence of both Gd and T34 showed healthier phenotypes and higher leaf and biomass production in comparison to untreated control plants or to plants that were inoculated with Gd only. Flowering and fruiting were also showed to be positively affected in plants

Biography:

Matthias Moerch has completed his Masters in Molecular Biotechnology at the Technical University of Munich in 2014, comparing different protein digestion methods for shotgun proteomics in his Master’s Thesis. Since 2015 he pursues his doctorate at the Department of Microbiology at the Technical University of Munich establishing the extreme thermophilic bacterium Thermus thermophilus as an alternative host for metagenome analysis.

Abstract:

The constant depletion of fossil energy sources and the raising demand for more eco-friendly alternatives challenges science to develop new technologies. The utilization of plant biomass is a promising substitute for conventional systems by being a rather inexpensive energy carrier and of high sustainability at the same time. Its availability through cultivation of energy crops and by usage of agricultural/forestry waste account for great industrial value. In particular, the valorisation of waste by converting it to fermentable substrates has the advantage not to threaten food security. Since plants themselves consist primarily of lignocellulosic fibres (a mixture of cellulose, lignin and hemicellulose), the first step in the process of fuel production is the hydrolysis of this bigger structures into smaller, more soluble sugars. Its depolymerization into glucose monomers is often facilitated by using cellulases – an enzyme group consisting of endoglucanases (EC 3.2.1.4), cellobiohydrolases (EC 3.2.1.91) and β-glucosidases (EC 3.2.1.21) which work synergistically together. With increasing market share of new bio fuels, the future demand for (novel) cellulases – which today already make up 8 % of worldwide industrial enzyme demands – will therefor rise as well constantly.

In this work we developed a system to select for thermostable glycoside hydrolase enzymes (GH) using the extremely thermophilic bacterium Thermus thermophilus. Unlike mesophilic bacteria (e.g. E. coli), T. thermophilus provides an overall more suitable enzymatic background and thereby greater potential to express thermostable recombinant proteins properly. This increases the probability of detecting novel thermostable cellulases when transformed in this organism; compared to the commonly used host E. coli.

As an advantage, growth-based selection approaches already result in favourable enzyme variants, compared to traditional screening methods which require testing of every single clone.

In order to obtain a GH-negative strain, we constructed a

T. thermophilus knock-out strain which lacks four glycosidases. As confirmed by para-nitrophenol (pNP) enzyme assays and incubation of cell extract with X-Gal and X-Glu, these deletions reduced the hosts ability to cleave β-glycosidic and β- galactosidic bonds to a minimum. Without these GHs, the knock out strain is not able to grow in minimal medium. Complementation with the hosts own β-glucosidase via the shuttle vector pMK18 re-established growth of the knock out strain. For purpose of following system verification, cglT – a glycosyl hydrolase belonging to GH family 1 from the thermophilic bacterium Thermoanaerobacter brockii – was transformed in the T. thermophilus knock-out strain. This novel approach of complementation-based selection in an extreme thermophilic organism is a promising tool to look through big meta genomes or mutagenesis libraries, selecting for enzyme variants of higher thermostability and/or other substrate specificity in a highly efficient manner.

Biography:

Nathita Phumthanakorn is a Ph.D. student from the Department of Microbiology, Veterinary Science, Chulalongkorn, Thailand.

Abstract:

The detection of 18 genes encoding cell wall-associated (CWA) proteins in Staphylococcus pseudintermedius named spsA-spsR were performed by using the new development of a set of multiplex PCRs (mPCRs). The distribution of these genes were detected in isolates from dogs (n=70), humans (n=25), and the environment of a veterinary hospital (n=40). The new 4 sets of mPCR comprising of 4-5 genes per set, including nuc gene as an internal control were developed. The mPCR sets could detect at least 1 pg/µl of DNA template. We found 23 sps gene profiles among the 135 isolates, with diverse gene combinations. spsD, spsF, spsI, spsO, spsP, and spsQ were variable detection but not statistically significant difference in each sources of isolates. Only spsP and spsQ encoded protein A or Spa were more frequently detected in the canine isolates from infected sites than from carriage sites suggested to play a role in pathogenicity. Interestingly, the positive amplicons of spsR gene in three human isolates showed gene deletions that were similar to the sequence in S. aureus ST398. The variation and difference of surface protein genes between human and animal S. aureus, including deletions, insertions, and truncation or pseudogenes have been reported and suggested to differentially affect host-specific adaptation.

Biography:

Miri Park has completed her master’s degree in life science from Korea University, Republic of Korea. She is the researcher of Ingredients and Solution Team at Lotte R&D center, Republic of Korea. She is responsible to search for useful food materials, especially probiotics, to evaluate efficacy and apply it to products.

Abstract:

Rotaviruses are the most important cause of diarrhea in infants and children worldwide. However, to date, no specific antiviral drugs for the treatment of rotavirus infection have been developed. We isolated Lactobacillus strains from the Korean traditional fermented food, Kimchi. Among them, Lactobacillus plantarum LRCC5310 strain, specifically, the exopolysaccharides(EPS) produced from the strain, were shown to have an antiviral effect against human rotavirus Wa strain in vivo. The oral administration of EPS led to a decrease in the duration of diarrhea, viral shedding and the destruction of enteric epithelium integrity in the infected mice. Also, to assess safety, oral administration to mice for 14 days had no adverse effects on liver, heart, stomach, lung, kidney and intestine through histology and blood analysis. The findings indicate that the strain L. platarum LRCC5310 does not raise safety concerns in mice, up to 5,000 ppm concentration. Thus, this EPS is likely to be safe for human consumption and it can be used for the effective control of rotavirus infection. Further studies in humans should be conducted.